6AC5: PDB entry 6AC5

Crystal structure of RIPK1 death domain GlcNAcylated by EPEC effector NleB. Determined by X-ray diffraction at 1.45 Å resolution. Released 1 May 2019.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 1
Atoms: 926
Mol. weight: 13.26 kDa
Ligands: NAG
Released: 1 May 2019

Explore 6AC5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AC5 contains 9 α-helices and 2 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	575-577	3
α-helix	580	1
β-strand	581	1	1
α-helix	582	1
α-helix	584-593	10
α-helix	599-604	6
α-helix	609-618	10
α-helix	624-643	20
β-strand	645	1	1
α-helix	646-655	10
α-helix	659-668	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-interacting serine/threonine-protein kinase 1	A	protein	111	Homo sapiens	Q13546 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6AC5_1 Receptor-interacting serine/threonine-protein kinase 1 (chains A)
NTNFKEEPAAKYQAIFDNTTSLTDKHLDPIRENLGKHWKNCARKLGFTQSQIDEIDHDYE
RDGLKEKVYQMLQKWVMREGIKGATVGKLAQALHQCSRIDLLSSLIYVSQN

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector. Ding, J., Pan, X., Du, L. et al. Mol Cell (2019) 74:922. DOI 10.1016/j.molcel.2019.03.028 · PubMed

Other PDB entries of the same protein (UniProt Q13546 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5ZMZ 1.4 Å, Amyloid core of RIP1
4ITJ 1.8 Å, Crystal structure of RIP1 kinase in complex with necrostatin-4
6NW2 2.0 Å, Structure of human RIPK1 kinase domain in complex with compound 11
7FD0 2.0 Å, Crystal Structure of human RIPK1 kinase domain in complex with a novel inhibitor
24IB 2.05 Å, Crystal structure of human RIPK1 kinase domain in complex with compound HR10
9Q31 2.05 Å, RIP1 kinase domain in complex with GDC-8264
6NYH 2.1 Å, Structure of human RIPK1 kinase domain in complex with GNE684
9GTY 2.15 Å, RIPK1 in complex with AZ"320
7FCZ 2.21 Å, Crystal Structure of human RIPK1 kinase domain in complex with a novel inhibitor
5HX6 2.23 Å, Crystal structure of RIP1 kinase with a benzo[b][1,4]oxazepin-4-one
4ITH 2.25 Å, Crystal structure of RIP1 kinase in complex with necrostatin-1 analog
9GTG 2.25 Å, RIPK1 in complex with AZ"902

Browse structure collections

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